/// <summary>
/// Validate Hierarchical Clustering for stage2 using kimura distance matrix and hierarchical method name
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="hierarchicalMethodName"></param>
private void ValidateHierarchicalClusteringStage2(string nodeName,
UpdateDistanceMethodsTypes hierarchicalMethodName)
{
Initialize(Constants.MuscleDnaSequenceNode, Constants.ExpectedScoreNode);
List<ISequence> stage1AlignedSequences = GetStage1AlignedSequence();
IDistanceMatrix matrix = GetKimuraDistanceMatrix(stage1AlignedSequences);
IHierarchicalClustering hierarcicalClustering = GetHierarchicalClustering(matrix,
hierarchicalMethodName);
ValidateHierarchicalClustering(nodeName, hierarcicalClustering.Nodes,
hierarcicalClustering.Edges);
ApplicationLog.WriteLine(String.Format(null,
@"PamsamBvtTest:: herarchical clustering stage2 nodes and edges generation and
validation completed success with different
hierarchical clustering method name {0}",
hierarchicalMethodName.ToString()));
}
/// <summary>
/// Validate Hierarchical Clustering for stage2 using kimura distance matrix
/// and hierarchical method name
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="moleculeType">molecule type of sequences</param>
/// <param name="hierarchicalMethodName">hierarchical method name</param>
private void ValidateHierarchicalClusteringStage2(string nodeName, MoleculeType moleculeType,
UpdateDistanceMethodsTypes hierarchicalMethodName)
{
switch (moleculeType)
{
case MoleculeType.DNA:
Initialize(Constants.MuscleDnaSequenceNode, Constants.ExpectedScoreNode);
break;
case MoleculeType.Protein:
Initialize(Constants.MuscleProteinSequenceNode, Constants.ExpectedScoreNode);
break;
case MoleculeType.RNA:
Initialize(Constants.MuscleRnaSequenceNode, Constants.ExpectedScoreNode);
break;
default:
break;
}
List<ISequence> stage1AlignedSequences = GetStage1AlignedSequence(moleculeType);
// Get kimura distance matrix
IDistanceMatrix matrix = GetKimuraDistanceMatrix(stage1AlignedSequences);
// Get hierarchical clustering using method name
IHierarchicalClustering hierarcicalClustering = GetHierarchicalClustering(matrix,
hierarchicalMethodName);
ValidateHierarchicalClustering(nodeName, hierarcicalClustering.Nodes,
hierarcicalClustering.Edges);
ApplicationLog.WriteLine(String.Format(null,
@"PamsamP1Test:: hierarchical clustering stage2 nodes and edges generation and
validation completed success for {0} moleculetype with different
hierarchical clustering method name {1}",
moleculeType.ToString(),
hierarchicalMethodName.ToString()));
}
/// <summary>
/// Validate Muscle multiple sequence alignment with different profiler and hierarchical clustering method name.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="expectedScoreNode">Expected score node</param>
/// <param name="hierarchicalClusteringMethodName">hierarchical clustering method name</param>
/// <param name="profileName">SW/NW profiler</param>
/// <param name="isWeightedProduct">True if it of the WeightedProduct type else false.</param>
private void ValidatePamsamAlignWithUpdateDistanceMethodTypes(string nodeName,
string expectedScoreNode,
UpdateDistanceMethodsTypes
hierarchicalClusteringMethodName,
ProfileAlignerNames profileName,
bool isWeightedProduct)
{
ValidatePamsamAlign(nodeName, expectedScoreNode, hierarchicalClusteringMethodName,
DistanceFunctionTypes.EuclideanDistance, profileName,
ProfileScoreFunctionNames.InnerProduct,
isWeightedProduct);
ApplicationLog.WriteLine(String.Format(null,
@"PamsamBvtTest:: Pamsam alignment validation completed successfully with different hierarchical clustering method name {0}",
hierarchicalClusteringMethodName.ToString()));
}
/// <summary>
/// Validate Muscle multiple sequence alignment with different profiler and hierarchical clustering method name.
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="moleculeType">molecule type of sequences</param>
/// <param name="expectedScoreNode">Expected score node</param>
/// <param name="hierarchicalClusteringMethodName">hierarchical clustering method name</param>
/// <param name="profileName">SW/NW profiler</param>
private void ValidatePamsamAlignWithUpdateDistanceMethodTypes(string nodeName,
MoleculeType moleculeType,
string expectedScoreNode,
UpdateDistanceMethodsTypes
hierarchicalClusteringMethodName,
ProfileAlignerNames profileName)
{
ValidatePamsamAlign(nodeName, moleculeType, expectedScoreNode,
hierarchicalClusteringMethodName, DistanceFunctionTypes.EuclideanDistance,
profileName, ProfileScoreFunctionNames.WeightedInnerProduct, kmerLength,
false, false);
ApplicationLog.WriteLine(
String.Format(null,
"PamsamP1Test:: Pamsam alignment validation completed successfully for {0} moleculetype with different hierarchical clustering method name {1}",
moleculeType.ToString(),
hierarchicalClusteringMethodName.ToString()));
}
